readers refactoring

tdefa · Apr 8, 2024 · 6fa79a4 · 6fa79a4
1 parent a92d155
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Default `min_transcripts` set in snakemake configs
 - Minimum number of transcripts per patch set to 4000 (#41)
 - Config files refactoring (configs added or renamed)
+- Readers refactoring
 
 ## [1.0.9] - 2024-04-03
 

diff --git a/docs/api/io.md b/docs/api/io.md
@@ -35,3 +35,11 @@
 ::: sopa.io.wsi
     options:
       show_root_heading: true
+
+::: sopa.io.uniform
+    options:
+      show_root_heading: true
+
+::: sopa.io.blobs
+    options:
+      show_root_heading: true
diff --git a/docs/api/utils/data.md b/docs/api/utils/data.md
diff --git a/docs/tutorials/api_usage.ipynb b/docs/tutorials/api_usage.ipynb
@@ -6,7 +6,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from sopa.utils.data import uniform\n",
     "import sopa.segmentation\n",
     "import sopa.io"
    ]
@@ -60,9 +59,9 @@
    ],
    "source": [
     "# The line below creates a toy dataset for this tutorial\n",
-    "# Instead, use sopa.io to read your own data as a SpatialData object: see https://gustaveroussy.github.io/sopa/api/io/\n",
-    "# For instance, if you have MERSCOPE data, you can do `sdata = sopa.io.merscope(\"/path/to/region_0\")`\n",
-    "sdata = uniform()\n",
+    "# To load your own data, such as MERSCOPE data, you can do `sdata = sopa.io.merscope(\"/path/to/region_0\")`\n",
+    "# For more details, see https://gustaveroussy.github.io/sopa/api/io/\n",
+    "sdata = sopa.io.uniform()\n",
     "\n",
     "sdata.write(\"tuto.zarr\", overwrite=True)\n",
     "sdata"

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -37,7 +37,6 @@ nav:
       - sopa.annotation.tangram: api/annotation/tangram.md
       - sopa.annotation.fluorescence: api/annotation/fluorescence.md
     - sopa.utils:
-      - sopa.utils.data: api/utils/data.md
       - sopa.utils.image: api/utils/image.md
       - sopa.utils.polygon_crop: api/utils/polygon_crop.md
     - sopa.embedding: api/embedding.md

diff --git a/poetry.lock b/poetry.lock
diff --git a/sopa/io/__init__.py b/sopa/io/__init__.py
@@ -1,8 +1,13 @@
-from .imaging import macsima, phenocycler, hyperion, ome_tif
 from .explorer import write, align
 from .standardize import write_standardized
-from .transcriptomics import merscope, xenium, cosmx
-from .histopathology import wsi, wsi_autoscale
+from .reader.cosmx import cosmx
+from .reader.merscope import merscope
+from .reader.xenium import xenium
+from .reader.macsima import macsima
+from .reader.phenocycler import phenocycler
+from .reader.hyperion import hyperion
+from .reader.utils import ome_tif
+from .reader.wsi import wsi, wsi_autoscale
 from .report import write_report
 
 from ..utils.data import blobs, uniform
diff --git a/sopa/io/imaging.py b/sopa/io/imaging.py
diff --git a/sopa/io/reader/__init__.py b/sopa/io/reader/__init__.py